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Formalize how channel types are shared between modalities that use channels.tsv files. #1436
Description
came up during the BEP029 (motion) community review:
also related to:
- [SCHEMA] Refactor channel types #1126
- Support full object definitions for valid values in schema #904
Some BIDS modalities allow for channels.tsv metadata:
- EEG
- MEG
- iEEG
- NIRS
channels.tsv files MUST have a type column that contains (upper case) strings from a defined vocabulary as specified in the modality specific sections. This column MUST be the second column in channels.tsv files.
In the schema, the valid values for type are specified separately for EEG, MEG, iEEG, and NIRS, see:
| type__eeg_channels: |
| type__meg_channels: |
| type__ieeg_channels: |
| type__nirs_channels: |
Even though in the spec, it says:
For EEG (types are shared with MEG and iEEG):
bids-specification/src/modality-specific-files/electroencephalography.md
Lines 217 to 219 in 741d4ef
| Restricted keyword list for field `type` in alphabetic order (shared with the | |
| MEG and iEEG modality; however, only the types that are common in EEG data are listed here). | |
| Note that upper-case is REQUIRED: |
For MEG (no mention of sharing):
bids-specification/src/modality-specific-files/magnetoencephalography.md
Lines 229 to 230 in 741d4ef
| Restricted keyword list for field `type`. | |
| Note that upper-case is REQUIRED: |
For iEEG (types are shared with MEG and EEG):
bids-specification/src/modality-specific-files/intracranial-electroencephalography.md
Lines 233 to 235 in 741d4ef
| Restricted keyword list for field type in alphabetic order (shared with the MEG | |
| and EEG modality; however, only types that are common in iEEG data are listed here). | |
| Note that upper-case is REQUIRED: |
For NIRS (types are shared with EEG, MEG, and iEEG -- see last sentence):
bids-specification/src/modality-specific-files/near-infrared-spectroscopy.md
Lines 197 to 207 in 741d4ef
| All NIRS channels types MUST correspond to a [valid SNIRF data type](https://github.com/fNIRS/snirf/blob/master/snirf_specification.md#appendix). | |
| Additional channels that are recorded simultaneously with the NIRS | |
| device and stored in the same data file SHOULD be included as well. | |
| However, additional channels that are simultaneously recorded with a different device | |
| SHOULD be stored according to their appropriate modality specification. | |
| For example, motion data that was simultaneously recorded with a different device should be specified | |
| according to BEP029 and not according to the NIRS data type. | |
| Whereas, if the motion data was acquired in with the NIRS device itself, it should be included here with the NIRS data. | |
| Any of the channel types defined in other BIDS specification MAY be used here as well such as `ACCEL` or `MAGN`. | |
| As several of these data types are commonly acquired using NIRS devices they are included as an example at the base of the table. | |
| Note that upper-case is REQUIRED. |
We should:
- clarify/formalize how channel types may be shared between modalities
- think about how to make this clearer in the schema and the associated rendering of channel type tables in the modality sections
I propose that channel types should be shared between all BIDS modalities.